Amino Acids Classification PDF

# Amino acids ## ILOS Students will be able to answer questions on the following topics: 1. Classification of amino acids based on structure 2. Based on side chain character 3. Based on metabolic fate 4. Based on nutritional requirements 5. Iso electric point 6. Reactions due to carboxyl group 7....

# Amino acids ## ILOS Students will be able to answer questions on the following topics: 1. Classification of amino acids based on structure 2. Based on side chain character 3. Based on metabolic fate 4. Based on nutritional requirements 5. Iso electric point 6. Reactions due to carboxyl group 7. Reactions due to amino group 8. Peptide bond formation ## Amino acids - Amino acids are the building units of proteins. - Proteins are polymers of L-$\alpha$-amino acids linked together by what is called "peptide bond". - There are about 300 amino acids occur in nature. Only 20 of them occur in proteins. ### Structure of amino acids: Each amino acid has 4 different groups attached to the $\alpha$-carbon (which is C-atom next to COOH): 1. Amino group. 2. COOH group. 3. Hydrogen atom. 4. Side chain (R). The structure of an amino acid is shown here: ``` H | H | HO - C - C - N | | R H ``` - At physiological pH (7.4), -COOH group is dissociated forming a negatively charged carboxylate ion (COO-) and amino group is protonated forming positively charged ion (NH3+) forming Zwitter ion. - N.B. Proline is an imino acid not amino acid (see latter) ## Classification of amino acids ### Chemical classification: - According to the number of COOH and NH2 groups i.e. according to net charge on amino acid: #### A- Monobasic monocarboxylic amino acids i.e. neutral or uncharged: ##### 1- Simple amino acids: - Glycine: R=H - Alanine: R=CH3 The structures of Glycine and Alanine are shown here: ``` H | H | HO - C - C - N | | H H | COO- Glycine Gly; G H | H | HO - C - C - N | | CH3 H | COO- Alanine Ala; A ``` ##### 2- Branched chain amino acids: R is branched such as in: - Valine: R=isopropyl gp - Leucine: R = isobutyl gp - Isoleucine: R = is isobutyl The structures of Valine, Leucine and Isoleucine are shown here: ``` H | H | HO - C - C - N | | CH3 H | COO- | CH-CH3 | CH3 Valine Val; V H | H | HO - C - C - N | | CH3 H | COO- | CH-CH3 | CH2 | CH3 Leucine Leu; L H | H | HO - C - C - N | | CH3 H | COO- | CH-CH3 | CH2 | CH3 Isoleucine Ile; I ``` ##### 3- Neutral sulfur containing amino acids: - e.g. Cysteine and Methionine. What is cystin? The structures of Cysteine and Methionine are shown here: ``` H | H | HO - C - C - N | | CH2 H | COO- | SH Cysteine Cys; C H | H | HO - C - C - N | | CH2 H | COO- | CH2 | S-CH3 Methionine Met; M ``` ##### 4- Neutral hydroxy amino acids: - e.g. Serine and Threonine The structures of Serine and Threonine are shown here: ``` H | H | HO - C - C - N | | CH2 H | COO- | CH2-OH Serine Ser; S H | H | HO - C - C - N | | CH2 H | COO- | CH2-OH | CH3 Threonine Thr; T ``` ##### 6- Neutral aromatic amino acids: - Phenyl alanine: It’s alanine in which one hydrogen of CH3 is substituted with phenyl group. So it’s called phenyl alanine - Tyrosine: - it is P- hydroxy phenyl alanine - Tryptophan: as it contains indole ring so it is classified as heterocyclic amino acid The structures of Phenyl Alanine and Tyrosine are shown here: ``` H2 | C | HO - C - C - N | | CH2 H | COO- Phenyl alanine Phe; F (Benzene group) H2 | C | HO - C - C - N | | CH2 H | COO- Tyrosine Tyr; Y (Phenol group) ``` ##### 7- Neutral heterocyclic amino acids: - Tryptophan: contains indole ring - Proline: In proline, amino group enters in the ring formation being a-imino gp so proline is an a-imino acid rather than a-amino acid The structures of Tryptophan and Histidine are shown here: ``` CH2 | CH-NH3 | COO- . Tryptophan (Trp) (W) with indole group CH2 | HN - N - CH-NH3 | | C H / \ / \ C C C \ / \ / C C C \ / \ / C COO- Histidine; His H (imidazole group) ``` #### B- Basic amino acids: - Contain two or more NH2 groups or nitrogen atoms that act as base i.e. can bind proton. - At physiological pH, basic amino acids will be positively charged. - e.g. - Lysine - Arginine: contains guanido group - Histidine: is an example on basic heterocyclic amino acids The structures of Aspartic Acid, Glutamic Acid, Lysine, Arginine and Histidine are shown here: ``` Electrically charged Acidic H | H | HN- C - C - O | CH2 | CH2 | COO- Aspartic acid (Asp) H | H | HN- C - C - O | CH2 | CH2 | CH2 | COO- Glutamic acid (Glu) Basic H | H | HN - C - C - O | CH2 | CH2 | CH2 | CH2 | NH3+ Lysine (Lys) H | H | HN - C - C - O | CH2 | CH2 | CH2 | N - NH2 - NH2 | NH+ Arginine (Arg) H | H | HN - C - C - O | CH2 | CH2 | N - NH2 - NH+ | | H C \ / C / \ C C | COO- Histidine (His) ``` #### C- Acidic amino acids: - at physiological pH will carry negative charge. - e.g. Aspartic acid (aspartate) and Glutamic acid (glutamate). ##### Aspargine and Glutamine: - They are amide forms of aspartate and glutamate in which side chain COOH groups are amidated. - They are classified as neutral amino acids. ## Classification according to polarity of side chain (R): ### A- Polar amino acids: - In which R contains polar hydrophilic group so can forms hydrogen bond with H2O. In those amino acids, R may contain: - OH group: as in serine, threonine and tyrosine - SH group: as in cysteine - Amide group: as in glutamine and aspargine - NH2 group or nitrogen act as a base (basic amino acids): as lysine, arginine and histidine - COOH group (acidic amino acids): as aspartic and glutamic. ### B- Non polar amino acids: - R is alkyl hydrophobic group which can't enter in hydrogen bond formation. - 9 amino acids are non polar (glycine, alanine, valine, leucine, isoleucine, phenyl alanine, tryptophan, proline and methionine) The structures of the polar and non-polar amino acids are shown here: ``` H | H | H3N+-C-C | | CH2 H | O OH Serine (Ser) H | H | H3N+-C-C | | CH | OH CH3 | O Threonine (Thr) H | H | H3N+-C-C | | CH2 H | O SH Cysteine (Cys) H | H | H3N+-C-C | | CH2 H | O | C / \ / \ C C \ / \ / C C \ / \ / C | OH Tyrosine (Tyr) H | H | H3N+-C-C | | CH2 H | O C / \ / \ C C \ / \ / C C \ / \ / C | NH2 O Asparagine (Asn) H | H | H3N+-C-C | | CH2 H | O C / \ / \ C C \ / \ / C C \ / \ / C | NH2 O Glutamine (Gln) Polar H | H | H3N+-C-C | | CH3 H | O Alanine (Ala) H | H | H3N+-C-C | | CH H | CH3 CH3 | O Valine (Val) H | H | H3N+-C-C | | CH2 H | O CH | CH3 CH3 | CH3 Leucine (Leu) H | H | H3N+-C-C | | CH2 H | O CH | CH3 CH3 | CH3 Isoleucine (Ile) Nonpolar H | H | H3N+-C-C | | CH2 H | O S | CH3 Methionine (Met) H | H | H3N+-C-C | | CH2 H | O | C / \ / \ C C \ / \ / C C \ / \ / C | NH Phenylalanine (Phe) H | H | H3N+-C-C | | CH2 H | O | C / \ / \ C C \ / \ / C C \ / \ / C | NH Tryptophan (Trp) H | H | H3N+-C-C | | H2C H | CH2 | CH2 | C / \ / \ C C C \ / \ / C C C \ / \ / C | O Proline (Pro) ``` ## Nutritional classification ### 1- Essential amino acids: - These amino acids can't be formed in the body and so it is essential to be taken in diet. Their deficiency affects growth, health and protein synthesis. - Valine, Leucine, Isoleucine, Threonine, Methionine, Lysine, Phenylalanine, Tryptophan ### 2- Semiessential amino acids: - These are formed in the body but not in sufficient amount for body requirements especially in children. - Histidine and arginine ### 3- Non essential amino acids: - These are the rest of amino acids that are formed in the body in amount enough for adults and children. They are the remaining 10 amino acids. ## IV- Metabolic classification: According to metabolic or degradation products of amino acids: ### 1- Ketogenic amino acids: - Which give Ketone bodies. - Lysine and Leucine are the only pure ketogenic amino acids. ### 2- Mixed ketogenic and glucogenic amino acids: - Which give both keton bodies and glucose. - These are: isoleucine, phenyl alanine, tyrosine and tryptophan. ### 3- Glucogenic amino acids: - Which give glucose. - They include the rest of amino acids. These amino acids by catabolism yields products that enter in glycogen and glucose formation. ## Physical properties: Amphoteric properties of amino acids: - Amino acids are amphoteric molecules: That is they have both basic and acidic groups and so can act as base or acid. - Neutral amino acids (monobasic, monocarboxylic) exist in aqueous solution as "Zwitter ion." They contain both positive and negative charge. Zwitter ion is electrically neutral and can't migrate into electric field. - Isoelectric point (IEP) = is the pH at which the zwitter ion is formed. - e.g IEP of alanine is 6 ## Chemical properties of amino acids: ### 1- Reactions due to COOH group: - Decarboxylation - Salt formation with alkalis. - Ester formation with alcohols. - Amide formation with amines and decarboxylation. ### 2- Reactions due to NH2 group: - Deamination. - Transamination. ### 3- Reaction due to the presence of active group in side chain (R) ### 4-Peptide bond formation ## Peptides and Proteins - 20 amino acids are commonly found in protein. - These 20 amino acids are linked together through "peptide bond forming peptides and proteins". - The chains containing less than 50 amino acids are called "peptides" while those containing greater than 50 amino acids are called "proteins". - Peptide bond formation: - The $\alpha$-carboxyl group of one amino acid forms a covalent peptide bond with the $\alpha$-amino group of another amino acid by removal of a molecule of water. - The result is: Dipeptide (i.e. Two amino acids linked by one peptide bond). By the same way, the dipeptide can then forms a second peptide bond with a third amino acid to give Tripeptide. Repetition of this process generates a polypeptide or protein of specific amino acid sequence. The formation of a peptide bond is shown here: ``` OH | Peptide bond OH | OH | SH | CH2 | CH2 | H | H-N-C-C - | | HO H | C / \ / \ C C \ / \ / C C \ / \ / C | OH ``` This structure shows a **dipeptide**. The amino and carboxyl ends of the peptide are also labeled. - Each polypeptide chain starts on the left side by free amino group of the first amino acid enter in chain formation. It is termed (N- terminus). - Each polypeptide chain ends on the right side by free COOH group of the last amino acid and termed (C-terminus). ## Multiple choice questions 1. All proteins contain the - (A) Same 20 amino acids - (B) Different amino acids - (C) 300 Amino acids occurring in nature - (D) Only a few amino acids 2. Proteins contain - (A) Only L-$\alpha$ amino acids - (B) Only D-amino acids - (C) DL-Amino acids - (D) Both (A) and (B) 3. The optically inactive amino acid is - (A) Glycine - (B) Serine - (C) Threonine - (D) Valine 4. At neutral pH, a mixture of amino acids in solution would be predominantly: - (A) Dipolar ions - (B) Nonpolar molecules - (C) Positive and monovalent - (D) Hydrophobic 5. An example of Sulphur containing amino acid is - (A) Methionine - (B) Leucine - (C) Valine - (D) Asparagine 6. An example of OH containing amino acid is - (B) Serine - (B) Leucine - (C) Valine - (D) Asparagine 7. At physiological pH, which type of amino acids are likely to carry a net positive charge? - o A) Neutral amino acids - o B) Acidic amino acids - o C) Basic amino acids - o D) Nonpolar amino acids - o E) Aromatic amino acids 8. Question: Which of the following amino acids is classified as essential - o A) Alanine - o B) Glycine - o C) Valine - o D) Glutamate - o E) Aspartate 9: Which amino acid contains an imino group instead of an amino group? - o A) Glycine - o B) Proline - o C) Tryptophan - o D) Serine - o E) Glutamine 10. Which of the following is classified as a ketogenic amino acid, generating ketone bodies during metabolism? - o A) Alanine - o B) Leucine - o C) Glutamate - o D) Serine ## Definitions - Define: Zwitter ion - Define Essential amino acids and list two examples. - Define Isoelectric point (IEP) - Define ketogenic amino acids and list two examples - Define peptide bond